FEASIBILITY OF THE VACCINE DEVELOPMENT FOR SARS-COV-2 AND OTHER VIRUSES USING THE SHELL DISORDER ANALYSIS
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Pacific Symposium on Biocomputing 2021
Feasibility of the vaccine development for SARS-CoV-2 and other viruses using the
shell disorder analysis
Gerard Kian-Meng Goh,1,* A. Keith Dunker,2 James A. Foster,3 and Vladimir N. Uversky4
1
Goh's BioComputing, Singapore 548957, Republic of Singapore (gohsbiocomputing@yahoo.com)
2
Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular
Biology, Indiana University School of Medicine, 410 W. 10 th St, HS5000,
Indianapolis, IN46202, USA
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3
Department of Biological Sciences University of Idaho, Moscow, ID 83843, USA
4
Department of Molecular Medicine,Morsani College of Medicine, University of South Florida, Tampa,
FL, USA
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Several related viral shell disorder (disorder of shell proteins of viruses) models were built using a disorder
predictor via AI. The parent model detected the presence of high levels of disorder at the outer shell in
viruses, for which vaccines are not available. Another model found correlations between inner shell
disorder and viral virulence. A third model was able to positively correlate the levels of respiratory
transmission of coronaviruses (CoVs). These models are linked together by the fact that they have
uncovered two novel immune evading strategies employed by the various viruses. The first involve the use
of highly disordered “shape-shifting” outer shell to prevent antibodies from binding tightly to the virus
thus leading to vaccine failure. The second usually involves a more disordered inner shell that provides for
more efficient binding in the rapid replication of viral particles before any host immune response. This
“Trojan horse” immune evasion often backfires on the virus, when the viral load becomes too great at a
vital organ, which leads to death of the host. Just as such virulence entails the viral load to exceed at a vital
organ, a minimal viral load in the saliva/mucus is necessary for respiratory transmission to be feasible. As
for the SARS-CoV-2, no high levels of disorder can be detected at the outer shell membrane (M) protein,
but some evidence of correlation between virulence and inner shell (nucleocapsid, N) disorder has been
observed. This suggests that not only the development of vaccine for SARS-CoV-2, unlike HIV, HSV and
HCV, is feasible but its attenuated vaccine strain can either be found in nature or generated by genetically
modifying N.
Keywords: SARS; COVID; disorder; Coronavirus; HIV; vaccine; virulence; viral shell.
1. Introduction
1.1. SARS-COV-2 Vaccine
Since its outbreak in December 2019, a dangerous coronavirus (CoV), severe acute respiratory
syndrome CoV-2 (SARS-CoV2), causing Coronavirus Disease (COVID-19) has spread rampantly
with the dire consequences including large numbers of deaths and morbidities [1]. The SARS-
CoV-2 spread has been so severe that many believe that it could only be kept in check with the
discovery and availability of effective vaccines. While the successes in the discovery of vaccines
for a large variety of viruses, including classical viruses, such as smallpox and rabies viruses,
© 2020 The Authors. Open Access chapter published by World Scientific Publishing Company and
distributed under the terms of the Creative Commons Attribution Non-Commercial (CC BY-NC) 4.0
License.
143Pacific Symposium on Biocomputing 2021
provide grounds for greater hope, optimism and inspiration toward the discovery of COVID-19
vaccines, there are also nightmare scenarios, in cases, such as HIV (human immunodeficiency
virus, HCV (hepatitis C virus), and HSV (herpes simplex virus), for which no vaccine has been
found despite searches that span close to 40, 30, and 100 years, respectively. The polio vaccine
development itself took 30-40 years, but those years were before the era of powerful modern
molecular technology. It would therefore be unfair to make such comparison [3,5]. A question is
then: Will the search for a SARS-CoV-2 vaccine be a nightmare as seen in HIV, or will it be a
spectacular success, as in the case of rabies and smallpox? We shall see that the shell disorder
analysis has much to say in this regard.
1.2. Shell disorder analysis of HIV and other viruses
In 2008, we reported that the use of artificial intelligence (AI) found some strange features in the
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outer shell (matrix) of the HIV-1, which was found to be very disordered [6]. We were not able to
detect this feature in any other virus, despite a search among of a somewhat wide variety of
unrelated viruses, such as influenza virus, rabies virus and the HIV's cousin, EIAV (equine
infectious anemia virus) [6]. In subsequent years, similar levels of disorder can be found in very
few other viruses, including HSV and HCV [2]. Both viruses are associated with sexual
transmission, and no effective vaccine has been found for both. These cannot be explained by
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current the standard textbook paradigm [2].
In these and similar studies, the levels of protein intrinsic disorder [7-12] were measured for
proteins constituting shell of each analyzed virus using a neural network-based predictor PONDR®
VLXT [13,14]. This algorithm predicts the intrinsic disorder predisposition of each residue in a
protein. A convenient yardstick to measure the level of disorder in a protein is PID (percentage of
disorder). In the case of HIV-1, the matrix PID reaches the high level of 70% [2].
1.3. Spinoff projects including coronaviruses: Shell disorder and modes of transmission
Following the success of the HIV shell project, several spinoff projects based on the similar
ideology were initiated. One of these spinoffs was the coronavirus project. Before the MERS-CoV
outbreak in 2012, a shell disorder model was built to predict the mode of transmission of this
virus based mostly on the levels of intrinsic disorder in its inner shell (N, Nucleocapsid) but also
partly taking into account the disorder status of the outer shell (membrane, M) [15]. When the
PIDs of M and N were measured for the variety of CoVs, the viruses were clustered into three
groups mainly based on their N PID values. Those with the highest PIDs are those with higher
respiratory but lower fecal-oral transmission potentials. Those with intermediate levels of N PIDs
are the CoVs predicted to have intermediate levels of both respiratory and fecal-oral transmission
potentials. The model was developed using knowledge of the behaviors of animal CoVs,
particularly porcine CoVs from the veterinary community [3] and was later further validated using
multivariate analysis [3,15,16].
In this model, SARS-CoV was placed in group B that contains CoVs with intermediate
respiratory and fecal-oral transmission potential and the results of the model were published in
2012 [15]. Upon the MERS-CoV (Middle Eastern respiratory syndrome CoV) outbreak, the
characterization and classification of MERS-CoV had to wait until the time when the genome or
proteome sequences of this virus became available. However, as soon as this information was
released, it was used to analyze MERS-CoV. This analysis revealed that MERS-CoV belongs to
the group C that contains CoVs with higher fecal-oral but lower respiratory transmission potentials
[16]. The results further validate the reliability of the model as clinical data of MERS-CoV do
show that it is not easily transmissible among humans via respiratory routes and is associated with
camels, which are often farmed and thus allow for greater fecal-oral transmission [17].
144Pacific Symposium on Biocomputing 2021
Yet another opportunity to validate the shell disorder model came with the COVID-19
outbreak. Again, the model was consistent with existing datae and placed SARS-CoV-2 in the
same category as SARS-CoV; i.e., CoVs with the intermediate levels of both respiratory and fecal-
oral transmission potentials [18]. There was, however, something noticeably odd about this virus.
Analysis showed that with the exception for HCoV-HKU1, SARS-CoV-2 had the hardest outer
shell (lowest MPID) in our fairly wide variety of CoVs analyzed then. This means that SARS-CoV-
2 is likely to resist the anti-microbial enzymes found in the saliva and mucus of the host and is
also likely to survive longer in non-physiological environments [19,20]. Further search has found
that such hardness is associated with burrowing animals, such as rabbits and pangolins that are in
contact with buried fecal materials [21,22]. Furthermore, clinical studies have shown that COVID-
19 patients shed large amounts of SARS-CoV-2 viral particles, which are far exceeding levels of
viral particles shed by infected with SARS-CoV [23]. The hardness of the outer shell and the
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ability of the virus to resist the anti-microbial enzymes in body fluids could account for these
observations
1.4. Yet another spinoff: Correlations between the inner shell disorder and virulence
Yet another spinoff from the parent HIV vaccine mystery project is the discovery of a correlations
between the inner shell disorder and virulence in fairly diverse set of related and unrelated viruses
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including Nipah virus (NiV), flaviviruses, Dengue virus (DENV), and Ebola virus (EBOV) [24-
28]. In this paper, we will address the feasibility of SARS-CoV-2 vaccine development based on
the shell disorder models and discuss the evolutionary aspects of SARS-CoV-2 and other viruses.
Figure 1. Virion Physiology A) HIV B) Coronavirus (CoV). (Figures reproduced with the permission of Gerard K.
M. Goh 2017)
2. Results
2.1. Clustering of CoV based mainly on NPID
As already mentioned, the CoV shell disordered model clustered CoVs into three statistically
identifiable groups (ANOVA p < 0.01, Table 1), which correlated positively with the levels of
respiratory transmission but negatively with the levels of fecal-oral transmission potentials. While
the main contributing independent variable is the NPID (r2=0.77, p < 0.01), a slight increase in the
correlation coefficient can be seen when both MPID and NPID are used as independent variables
(r2=0.80, p < 0.01). This implies that MPID does contribute to the model even if slightly. Figure 1
provides schematic virion physiology, with HIV and CoV as examples[3,4]. The inner and outer
shells of CoV is the N and M proteins, respectively, as seen in Figure 1B.
145Pacific Symposium on Biocomputing 2021
Table 1. Categorization of coronaviruses by mainly N PID to predict levels of respiratory and fecal-oral
transmission potentials ( p< 0.001, r2 = 0.8).
Shell Coronavirus Accession Code Accession Code M NPID Remarks
Disorder (M Proteins)a (N Proteins)a PID
Group
A HCoV-229E P15422(U) P15130(U) 23 56 Higher levels of
IBV(Avian) P69606(U) Q8JMI6(U) 10 56 respiratory
transmission
lower levels of
fecal-oral
transmission
B Bovine P69704(U) Q8V432(U) 7.8 53.1 Intermediate
Rabbit H9AA37(U) H9AA59(U) 5.7 52.2 levels of
PEDV (Porcine) P59771(U) Q07499(U) 8 51 respiratory and
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Canine (Resp.) A3E2F6(U) A3E2F7(U) 7 50.5 fecal-oral
HCoV-OC43 Q4VID2(U) P33469(U) 7 51 transmission
SARS-CoV P59596(U) P59595(U) 8.6 50.2
HCoV-NL63 Q6Q1R9(U) Q6Q1R8(U) 11 49
SARS-Cov-2 P0DTC5(U) P0DTC9(U) 5.9 48.2
Batsb A3EXD6(U) Q3LZX4(U) 11.2+5.3 47.7+0.9
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C MHV(Murine) Q9JEB4(U) P03416(U) 8 46.8 Lower levels of
Pangolin-CoVc QIA428617(G) QIA48630(G) 5.6+0.9 46.6+1.6 respiratory
MERS-CoV K0BU37(U) K0BVN3(U) 9.1 44.3 transmission
TGEV(Porcine) P09175(U) P04134(U) 14 43 higher levels of
Canine (Ent.) B8RIR2(U) Q04700(U) 8 40 fecal-oral
HCoV-HKU1 Q14EA7(U) Q0ZME3(U) 4.5 37.4 transmission
a
UniProt(U): https://www.uniProt.org; Genbank-NCBI(G): https://www.ncbi.nlm.nih.gov/protein
b
3 out of 4 bat-CoVs are in group B. Note: Large standard deviation can be seen for NPID as denoted by “+”
c
2 out of 3 pangolin-CoVs are in group C. One is almost identical to SARS-CoV-2 in N PID. All samples were
found to have high sequence similarities to the corresponding proteins found in SARS-CoV-2
2.2 Outer shell disorder is an indicator for the presence or absence of effective vaccines
While disorder at the inner shell is correlated with the mode of transmission, high outer shell
disorder is associated with difficulties in finding effective vaccines. We shall see later that
disorder at the inner shell (and sometimes at the outer shell as well) correlates with virulence.
Tables 2-3 summarize the disorder of the different shells of a variety of related and non-related
viruses. There are no effective vaccines for HIV, HCV and HSV, which have abnormally high
outer shell disorder. Conversely, viruses for which effective vaccines are available have ordered
outer shells. These include rabies, yellow fever virus, smallpox virus and rotavirus [2-4,29]. The
poliovirus has a capsid that is made up of a complex of several proteins, which are all relatively
ordered. As aforementioned, the effective vaccines for polio have been available since the 1950s
[4,5].
Table 2. Viruses and their descriptions. UniProt (http://www.uniprot.org) accession codes for shell proteins
are given.
Virus Virus Type, Outer Shell, Proteins Intermediate Inner Shell
Tansmission (UniProt Accession)* Shell
EIAVa Retroviridae (RNA) Matrix, p15 (P69732) Capsid, p26 Nucleocapsid,
Insect (P69732) p11(P69732)
FIVb Retroviridae, Fights, Matrix, p15 (P16087) Capsid, p24 Nucleocapsid.
Blood contacts (P16087) p13 (P16087)
HIV-1 Retroviridae Matrix, p17 Capsid, p24 Nucleocapsid,
Sexual (P03348) (P03348) p7(p17)
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HIV-2 Retroviridae Matrix, p17 Capsid, p24 Nucleocapsid,
Sexual, Bite (P04584) (P04584) p7(P04584)
Variola/ Poxviridae (DNA) Membrane, C9L(Q76U97), Core,
Smallpoxc Inhalation A14(P33839), F5(P33865) VP8(Q0N570),
4A(Q0N532),
4B(Q0N539)
Rabies Rhabdopviridae Matrix, M(P25224) Nucleocapsid,
(RNA) Bites N(P151979)
Poliovirus Picornaviridae Capsid, VP1-4
(RNA) Fecal-Oral (P03302)
Yellow Flaviviridae (RNA) Membrane, M Capsid, C
Fever (YFV) Insect (P03314) (P03314)
Rotavirus Reoviridae (RNA) Outer Capsid , VP7 Capsid, VP6 Capsid, VP2
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Fecal-oral (P21285) (P03530) (P12472)
SARS-CoV-2 Coronavirus Membrane Nucleocapsid
(RNA)Respiratory, (A3EXD6) (Q3LXZ4)
Fecal-oral
Hepatitis C (HCV) Flaviviridae Core, p19, p21
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(RNA) Sexual (P26663)
Herpes Tegument, VP22-UL49 (A74K33), Capsid, VP5
Simplex VP1/2-UL36 (I1UYK0), VP13/14- (p89442)
Virus-2 UL47 (A7LK25), VP16-UL48
(HSV-2)c (P68335), US3 (P13287)
a
Equine Infectious Anemia Virus (EIAV)
b
Feline Immunodeficiency Virus (FIV)
c
Only major shell proteins are considered
2.3. A disordered outer shell provides an immune evasion tactic: Viral shapeshifting
Evidently, as seen in Tables 2-3, some viruses like HIV evade the immune system via their
disordered outer shell. The question is then: How do viruses do it? Figure 2 summarizes the
mechanism of immune evasion as seen in the case of HIV and its disordered matrix. The
disordered matrix allows for motions that increase the movements of the surface glycoproteins
such that the antibodies are not able to bind firmly to the virus. In the case of HIV, HIV antibodies
can easily be found but neutralizing antibodies are difficult to find [2,3]. There are obviously
various degrees of vaccine failures that depends on the level of outer shell disorder as we shall see
in the case of FIV.
Table 3. Disorder levels (PID) of shell proteins. PIDs are arranged according proteins as stated in Table 2.
Effective vaccines have been discovered for EIAV, rabies, polio, smallpox and rotavirus.
Virus PID of PID of Intermediate PID of
Outer Shell Shell Inner Shell
EIAV 13+0.1 29+0.1 26+0.1
FIV 53.3+2 38.8+2.7 64.5+11.8
HIV-1, SIVcpz 56.5+10.8 44.5+2.6 39.5+3.0
HIV-2, SIVmac 51.5+2.5 26.6+2.9 46.5+0.1
Smallpox+ 13+0.1 8+0.1 19+0.1
15+0.1 4+0.1 12+0.1
Rabies 25.8+1.4 21.5+0.8
Poliovirus+ 34+3.8 15.12+6.1
31.3+3.6 27+0.1
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Yellow Fever (YFV) 35.2+0.9 74.3+0.9
Rotavirus 12.9+1 9.8+1.4 19+1.7
SARS-CoV-2 5.9+0.1 48.2+0.9
HCV+ 52.5+0.5 48.5+0.5
HSV-2 61+2 18+0.1
50+0.1
38+1
39+0.6
37+0.1
*The standard error is denoted by “+”
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Figure 2. Viral “shape-shifting” immune evasion. Highly disordered matrix allows for greater motions at the
glycoprotein that will prevent the antibodies from binding tightly to the virus. (Figure reproduced with the permission
of Gerard K. M. Goh 2017)
2.4. SARS-CoV-2: Exceptionally hard shell (low MPID) associated with burrowing animals and
buried feces
While Table 2 shows that it is difficult to find vaccines for viruses with extremely high levels of
disorder in outer shell, Figure 3A reiterates that even though virtually all CoVs have relatively
hard outer shell (for them, the fecal-oral transmission is generally an important route) SARS-CoV-
2 has an exceptionally hard outer shell ie low MPID. As a matter of fact, it has one of the hardest
outer shells (among all the CoVs). A later search for CoVs with harder (low disorder) M protein
came up with rabbit-CoV and pangolin-CoVs (see Table 1) [21,22]. There were obvious
associations with burrowing animals that are likely in contact with buried feces. It should also be
noted that while pangolin-CoVs were found to be closely related to SARS-CoV-2, the rabbit-CoV
is not. Independent but parallel evolutions with similar evolutionary pressures are implied in the
case of SARS-CoV-2 pangolin-CoVs, and rabbit-CoV [21,22].
148Pacific Symposium on Biocomputing 2021
A
PID
1!61
20
60
1 Outer Shell
15 50 I Intermediate
EJ
Dinner
40
10 30
20
11111111
Bat-HKU4 MERS-CoV Bo>ine SARS-CoV-2 HCOV-HKU1
10
0
HIV-1 HIV-2 FIV EIAV
HCOV-229E HCOV-NL63 SARS-CoV Canine (Resp) Rabbit
CPID
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I!!I
70
60
60
1 Outer SheD 50
50 I Intermediate
Dinner 40
40
30
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30
20
20
10
•
10
I SARS2 DENV TBEV-FE
HIV-1 SARS1 SARS2 SARS1 ZIKV TBEV-Si YFV
.- SARS-CoV-1/2 • - Flaviviruses
CFR: 9-10% 2-6% 50% Case-Fatality
(CFRl
Figure 3. Quantification of shell disorder in different viruses. A) PIDs ofM by CoV. SARS-CoV-2 has among the
hardest M ie lowest Mpm. B) Shell disorder of selected retroviruses. C) Comparative shell disorder. SARS-CoV-2
(SARS2). 2003 SARS-CoV (SARI). D) Inner shell disorder vs. virulence. Flavivirus capsid, C (inner shell. Case-
fatality rate (CFR)
2.5. Behavior of the animal hosts matters in the evolutions of the viruses: EIAV vs. HIV
While it has been seen that higher outer shell disorder and the absence of effective vaccines are
not just seen in retroviruses but also in other viruses, such as HCV and HSV as shown in Table 2,
Figure 3B illustrates that not all retroviruses have high matrix disorder or lack effective vaccines,
EIAV has ordered shells at all levels, and an effective vaccine for this virus was discovered in
1973 or before [30]. It should also be noted that HIV is predominantly sexually transmitted,
whereas EIAV is transmitted by blood sucking horseflies, which hold its blood meal in their
mouthpiece where the virus is exposed to the insect's saliva [2]. Unlike HIV, the EIAV needs the
hard (low disorder) shells to protect itself against destructive effects arising from the anti-
microbial enzymes found in the saliva. The "viral shape-shifting" immune evasive characteristic
found in HIV is therefore absence in viruses, such as EIAV and rabies viruses. Experimental
observations of outer shell disorder and the resulting immune evasion have been made [31-34].
2. 6. Feasibility of developing attenuated vaccine strains for SARS-Co V-2
We have seen that SARS-CoV-2looks nothing like the viruses, for which the effective vaccines
are unavailable. Furthermore, it has one of the hardest outer shells among CoVs (Figure 3A).
Figure 3D suggests that the attenuated vaccine strains can be obtained by lowering the disorder
levels in its inner shell; i.e., Nprn. Flaviviruses are used here only as an example of the evidence of
correlation [24.26]. While only correlations between flavivirus inner shell disorder and virulence
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are shown, a variety of other viruses have been found to have such characteristics. These include
NiV, EBOV and DENVs [24-28]. SARS-CoV-2 and the 2003 SARS-CoV do also provide hints of
such correlation by having respective NPID of 48% and 50%, while also having CFR of 2-6% and
9-10%, as seen in Figure 3C. The HIV and other viral shape-shifters exhibit a unique immune
evading tactic as seen in Figure 2, SARS-CoV1/2, NiV, EBOV, and flavivirus use a different
tactic, “Trojan Horse”, where the virus would replicate rapidly upon infection before the host
immune system even recognizes its presence [3].
3. Discussion
3.1. Links between respiratory transmission, N (Inner shell) disorder, and virulence: Viral load
in body fluids vs. vital organs
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A puzzle arises when we inspect the data shown in Table 1 and Figure 3D. In fact, Table 1 tells
us that there is a strong positive correlation between the inner shell disorder and respiratory
transmission potentials of CoV, whereas Figure 3D reports positive correlations between inner
shell disorder and virulence. What is then the connection between these two types of correlation?
They are connected, because they are related to viral loads at different parts of the body. In order
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for respiratory transmission to be feasible, a minimal level of viral load in the saliva or mucus has
to be attained. Similarly, death often occurs when the viral load in a specific vital organ exceeds a
minimal threshold. What could then account for the discrepancy between viral loads in body fluids
and vital organs? One answer is related to the ability of the virus to resist the anti-microbial
enzymes found in saliva and mucus. Given this and the anti-microbial resistant hard (low disorder)
outer shell of SARS-CoV-2, the significance of the observation that SARS-CoV-2 sheds high
amount of viral particles without increase in virulence, when compared with SARS-CoV is
reiterated.
3.2. Greater disorder in the inner shell proteins provide means for the more efficient replication
of viral particles
It has to be kept in mind that inner shell proteins have varied but similar functions across virus
species [4]. This accounts for the observation of correlations between inner shell disorder and
virulence across virus species. For instance, N proteins of CoVs are involved in assembly of
various viral proteins near or at the endoplasmic reticulum (ER) and Golgi apparatus in
preparation for packaging [35,36]]. Similarly, the C protein precursors of flaviviruses move
towards the ER and bind to its membrane, where interactions of other viral proteins take place in
the assembling of viral particles [4]. In the case of EBOV, the NP (nucleoprotein) helps forming a
tube-like structure that assists in the transportation of viral proteins to the ER [37]. As for the
NiV, the N protein binds to both L and P proteins to form the RNA polymerase [38], which is
responsible for the viral RNA replication. The inner shell proteins therefore play important roles in
the rapid replication of the viral particles. As we can see, instances of protein-protein/DNA/RNA
interactions taking place are aplenty. The greater the disorder, the more efficient the inner shell
protein is able to play its role in the replication of the virus as disorder provides for more effective
protein-protein/DNA/RNA binding [7,18,39].
3.3 Two modes of immune evasion: “Trojan Horse” (inner shell disorder) and “viral shape-
shifting” (outer shell disorder)
We have just described “Trojan Horse” immune evading strategy, where the virus replicates
rapidly via inner shell disorder, before the host immune system could even recognize it.
Oftentimes, such strategy backfires on the virus especially when the viral load overwhelms viral
organs and thus killing the host. We have also described the other immune evading strategy,
150Pacific Symposium on Biocomputing 2021
“viral shape-shifting” in HIV as manifested in the outer shell disorder (Figure 2), there is
evidence that HIV actually employs both strategies. This is complicated by the fact that the matrix
(outer shell) assumes many of the roles that inner shell proteins of other viruses would normally
have. These roles include embedding the proteins into the host membrane and assembling the viral
proteins [4]. Evidence of HIV's adoption of such strategy can be seen by the fact over 90%
patients infected by HIV-1 dies within two years of infection but the onset of symptoms (AIDS)
for HIV-2 and FIV may take may years if at all [6,40,41]. Unsurprisingly, the maximal matrix
PIDs of HIV-1, HIV-2 and FIV are 70%, 55% and 55% respectively (Figure 3B).
3.4. FIV, HIV-1 and HIV-2: Similarities and differences
As it was already mentioned, the “viral shape-shifting” immune evading strategy requires high
outer shell disorder, as seen in HIV, HSV and HCV. This, too, presents an enigma, as HIV-1,
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HIV-2, and FIV have different degrees of outer shell disorder (70%, 55%, 55%, see Figure 3B).
HIV-1 is spread globally via sexual transmission. While HIV-2 is also predominantly sexually
transmitted, it is mainly found in parts of Africa near its rainforest reservoir of the monkey, sooty
mungabey, which replenishes the virus by bites and other human interactions [41]. Similarly, FIV
is predominantly spread through fights and subsequent blood contacts [40]. These could explain
the discrepancies in levels of matrix disorder between HIV-1 and FIV/HIV-2.
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3.5. FIV vaccine enigma: Questionable efficacy
While there are apparent differences in evolution and matrix disorder of EIAV, HIV-1, and FIV,
there are also differences in the successes with respect to the search for their vaccines. The search
for an HIV vaccine has been ongoing for nearly 40 years with abysmal failures, but an effective
vaccine for its horse cousin, EIAV, was discovered in 1973 or before [30]. It was tested on 60
million horses and was able to deflect an oncoming pandemic. Needless to say, the matrix PID of
EIAV is 13%, compared to the HIV-1 MPID of 70%. A more enigmatic story can be found in the
case of FIV. A ray of hope came in 2002, when a FIV vaccine became commercially available. It
initially boasted of 82% efficacy against the FIV subtype A, but was later shown to be totally
ineffective against strains from countries, such as United Kingdom. It was shown to provide only
58% protection for cats in Australia [42]. Finally, the vaccine was later withdrawn from the
market in USA and Canada partly because of its questionable efficacy [40]. This is consistent with
our data showing that FIV (matrix PID = 55%), like HIV-2, has more moderate matrix disorder
than HIV-1.
4. Conclusions
4.1. Development of the SARS-CoV-2 vaccine is feasible and vaccine strains can be found in
nature
The nightmare scenario in the frantic search for the SARS-CoV-2 vaccine would be that it all ends up
like the search for the HIV vaccine or, even worse, FIV vaccine. However, we can all have a sigh of
relief as the shell disorder models are unable to detect any similarities between SARS-CoV-2, HIV-1
and FIV in terms of the outer shell disorder or peculiarities of evolution with respect to their modes of
transmission. The outer shell disorder of SARS-CoV-2 and SARS-CoV resembles more viruses, like
rotavirus, for which there are effective vaccines. Unlike rotavirus that is solely reliant on fecal-oral
routes, SARS-CoV-2 has a somewhat disordered inner shell. The presence of such feature is necessary
for most viruses with respiratory transmission potentials, because, as already explained, a minimal
viral load in the mucus or saliva is required for transmission. The higher inner shell disorder also
provides means for the “Trojan horse” immune evasion. Because of this, strategies involving
attenuation of the SARS-CoV-2 by creating N with greater order levels can be contrived. In fact, a
previous study has suggested that a SARS-CoV-2 precursor could have entered the human population
151Pacific Symposium on Biocomputing 2021
via pangolins in 2017 or before as an attenuated mild virus as a result of the peculiarities of the
behaviors of pangolins [21,22]. Therefore, the disorder analysis not only suggests that vaccine
development for SARS-CoV-2 is viable but also points out that the attenuated vaccine strains can
already exist in nature.
5. Materials and Methods
As already mentioned, protein intrinsic disorder is an important concept that can be used for various
analyses of proteins. It basically refers to the protein regions or entire proteins that have no unique 3D
structures. Disorder in proteins plays an array of significant roles, such as the recognition of binding
sites [7-12]. AI has been successfully employed to recognize disordered regions. For instance,
PONDR® VLXT (www.pondr.com) [11,12,43] deploys neural networks to recognize such regions, as
by 72.108.27.165 on 12/02/20. Re-use and distribution is strictly not permitted, except for Open Access articles.
it was trained using known disordered and ordered sequences. PONDR® VLXT has been successfully
used in the study of structural proteins of a variety of viruses including HIV, HSV, HCV, NiV,
EBOV, 1918 HIN1 influenza A virus, CoVs, DENV, and several flaviviruses, e.g., Yellow fever virus
(YFV), and Zika virus (ZIKV) [1-3,6,15,16,21,22,24-28,44]]. The reason that PONDR® VLXT is
highly suitable for the studies of structural proteins of viruses has to do with its sensitivity in detecting
Biocomputing 2021 Downloaded from www.worldscientific.com
local sites for potential protein-protein/DNA/RNA/lipid interactions [45]. A useful ratio used in this
study is PID (Percentage of Intrinsic Disorder), which is defined as the number of residues predicted
to be disordered divided by the total number of residues in the protein and multiplied by 100%. The
value of this parameter provides an estimate of the extent of disorder in the protein of interest. A
relational database was built using MYSQL, JDBC and JAVA. A JAVA program imports the
sequence and disorder information into the database [44]. Sequence information are obtained from
UniProt (http://www.uniProt.org) Multivariate analyses were done using R-statistical package [46].
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